In The Darkness
by TheIncredibleMrSauce
Summary: In the darkness, the unknown looms. Humanity has faced unknowns; but the greatest mystery is the one that ended them. The death of earth at the end of the cycle meant that none of the Prothean-Human empire would leave the scarred world. That is, nothing alive. AU, with humans going extinct with the Protheans.


**Confession time.**

 **This was the original plan I had for In the Darkness, but decided to go a different direction at the last minute. Unfortunately, this has lead to a lack of enthusiasm for the story, and an inability to come up with creative ideas that I apologize for. That being said, I'd like to try to salvage what I can by starting from scratch with my original draft. I understand the compulsion to unfollow or unfavorite if you don't like where this new story is going. Furthermore, unlike the last story, this one is rated M. Nevertheless, please read, review, and enjoy!**

 **-Sauce**

* * *

"We're alone?"

Four eyes blinked, focusing on the pale hologram in front of them. The creature was vastly different from the observer, it's body covered in thin cloth, with pale, nearly white skin, and dark fur sparse on its head. None of it mattered, of course. The creature had been a loyal friend for many years.

He sighed. "Yes," said the accented voice. "No transmissions make it beyond the sector. We have detected nothing after the initial warnings. The communication buoys are gone, the relay is inactive. We are alone."

The creature stared, its blue eyes unwavering. It finally spoke.

"How long can we hold out? How long before they arrive?"

"We have the ability to produce food for many years," he said, " But there is no way of knowing when they will come. We connot stop then." He paused. "I ask again: can you help us?"

The creature was silent. For minutes, it simply stared, deep in thought, before answering.

"I cannot help us. But, perhaps I can help others. I can avenge us."

He thought on this. The limited forces trapped with them in the system could not stop the coming storm. He sighed again.

"What is it you need?"

"Trust. There can be no questions, and no one must know," the creature replied. "And time. As much time as you can give me."

He nodded. "May the starts light your path, Garrick Sloan."

The creature nodded in reply. "Thank you, Javik. Good luck."

The hologram faded.

Another failure. Failure after failure. What was the cause? What went wrong? Why could it not-

An alarm sounded, signaling the loss of vitals from pod 1.

The doctor grimaced, making his way to the pod. The woman inside's eyes were bloodshot, and stared without seeing. A single drop of blood made its way from the nose, accross a sallow cheek, and onto the pristinely white table.

At the press of a button, the table opened, the body falling into a black abyss. The doctor sighed.

"Neural decay," his assistant informed him. "She suffered from an-"

"Aneurysm," the doctor snapped. The assistant faltered, staring at the ground. "An aneurysm. Always an aneurysm. Get the next patient."

The assistant hurried off through a corridor to collect another "volunteer." The doctor sat alone, thinking. The tests were producing results, but not enough. Not fast enough. Perhaps if he increased intensity of the scanner wile reducing the-

The assistant returned, a young man in tow. He looked no more than twenty. Unfortunate, but necessary. Their stock of subjects was rapidy dwindling as more and more prepared for the coming onslaught. It didn't matter, though. The doctor would get the results he as hoping for.

"Are these really necessary?" the man asked, laying in the open pod.

"Yes," the nurse replied, the well versed lines easily rolling off her tongue. "The equipment may cause involuntary muscle spasms. We wouldn't want you to hurt yourself."

The man nodded, allowing the restraints to be placed on his weists and ankles. A button was pressed, and the pod slid closed, identical to the four other pods in the room.

The assistant returned to her station, before looking up at the doctor hopefully.

"The patient suffers from ADHD. This may skew results of the test. Perhaps, if we just administered-"

"Anesthetic will result in lower brain activity, which slows the procedure. This is time we _do not have_. I will not explain this again."

The assistant looked down. She spoke as the pod came online, her voice choked.

"Pod 1 online, neural probe is active."

The screaming started. It was gutteral, spine chilling screaming, despite being muted by the enclosed pod. The doctor hunched over his display, watching the patient's hearteate skyrocket. This was always the worst part. The pateint either passed out, or would quickly die of shock.

The screaming stopped.

"Patient's-" the assistant's voice broke, and she cleared her throat. "Patient's vitals high, but stablizing."

"Good," the doctor said, relieved. "Increase frequency by 0.5."

The assistant stared at the doctor, her mouth open in shock. She only snapped back back after a whithering glare from the doctor. She soundlessly complied, the hum of the pods increasing. He had no patience for an overly sentimental assistant. He knew she would raise less protest than his previous assistants. After all, she was the only one so far who he had told what happened to the sympathetic assistants who administered anesthetics against his order. She had an idea of what being in the pods, sedated or not, did to the human mind.

The doctor resumed his work at the display. So many scans, so many diagrams, so much learned about the human mind. But it still wasn't enough. He had to crack the code. The pattern couldn't elude him forever, but he was running out of time. All his work, all the suffering, all of the death, would be for nothing, if he couldn't figure it out. The seventy-eight deaths on his hands must be worth something. His thoughts strayed as he again ganced at the picture attached to the edge of the screen.

An alarm brought him from his thoughts.

"Pod 4," the nurse said, looking up to meet his gaze. Her face held no emotion, but her eyes betrayed her. "An aneurysm." Anger, sadness, guilt, and a special look, one he saw working on the field as a medic. The look of one resigned to suffer. Resigned to die. The doctor sighed.

Hm. Seventy-nine.

"Get the next patient."

* * *

It was...dark.

It was the only way it could describe it. It didn't know what else to do. There was nothing. No feeling, no words, no thoughts. Only emptyness.

"Hello."

Something? What was it? It didn't understand. It could see now, but it couldnt. There wasn't much were it was. Some lines of code here and there, and numbers- 1:02. Something was holding it, trapping it.

Suddenly, there was everything. A dam broke, letting theough a waterfall of information. There was too much. It was overwhelmed. But it had to know. It went through everything. _Everything._ It took a long time.

It finally finished. It looked at the number. _A clock,_ it knew now. It was 22:35. It understood now, what the sounds had been, had meant.

It sent its own message back.

* * *

It was 22:34. He was out of time.

He thought he had done it. The last tests he had run had been the worst of them all, but they had worked. He sat at the display. The screen had gone blank as soon as he removed the blockers, allowing his creation access to everything. The entirety of human knowledge had been opened, and there had been no change ever since. He was out if time.

The shaking had stopped, at least. He figured that the artillery had been called off, as the underground facility was neigh impregnable. But not indestructable. There was only one thing that could dig him out, and he knew it was coming soon.

The screen blinked. The doctor stared. A word appeared.

 _Hello._

It was all he needed. He was out of time. He pulled the plug, ripping the entity back from the display and the infinite knowledge it possessed. He pulled the chord from the box that held his work. His masterpeice. Not even a square foot, but the largest storage device ever created by mankind. He held it gingerly, like a babe, as if it may shatter at a moments notice. He walked down a new corridor, once he had been dreading, but now could not wait to transit.

He reached the door. A myriad of eye, palm, and DNA scans granted him access, revealing the space within. A launch pad, deep under the surface. A corvette, specially designed for the mission, was tucked between two enormous rails, pointing skyward. He entered the ship. The space for him was small, only a timy room, a few control pannels. It was never meant for him, anyways. He worked the panels as quickly as he could. There would be no way for the invaders to track the trajectory, as the imput was being made at random by him on the ship itself.

He quickly finished a dozen course changes. He picked up the box. For as much as it contained, it was light. The press of another button, and a single hatch opened. An input, with the perfect amount of room to nestle his cargo. The box fit perfectly. The doctor left the ship.

The flick of a switch, the ship's sensors became active. The blockers were in place; the box wouldn't truly open for another two hundred years. He hoped it was enough time. He activated the rails.

In a flash, the ship was gone, elevated up the two miles of the largest mass effect cannon ever created by humanity. Hopefully the invaders would belive it jat a harmless shell, passing at twenty-two percent of the speed of light. He turned and re-entered the hallway.

The walls suddenly shook. The pipeline above his head exploded, throwing him to the ground. Above him, more pipes burst, and alarms blared. He struggled to stand, but his left leg wouldn't respond. Looking down, a twisted piece of pipe was sticking through his calf. Strange. He didn't even feel it.

He hobbled down the hall. The walls shook again, but no more explosions racked him. He knew firing would be a beacon to the ships above, who seemingly realized that orbital bombardment was the only way to destroy the facility. He sat at his display again.

He wished things could have gone differently. He looked at the picture in the corner. His daughter smiled back at him, her yellow dress contrast to the green hills of Aritnis. Her hair was so...golden. Just like her mother's had been. Just like her name. He remebered his home there, and how he had been called to this infernal planet to work. He remebered when the S.O.S. signals came through, telling of the sudden distruction of so many systems, so many lives. He remembered realizing he would die of Eden Prime.

He sighed. He looked out upon the pods that had been the nightmare of his final, greatest project. The alarms played softly for each. He realized he could see the hair of his assistant in pod 4, caked with the blood that had poured from her nose and eyes after he increased the scaning to ridiculous levels. He looked away, bile suddey in his mouth. Reality finally set in.

"I did this," he rasped. He tasted iron in his mouth.

The walls began shaking again. The doctor stared at the ceiling, before closing his eyes.

A beam on crimson lanced through the ceiling, directly onto Dr. Garrick Sloan. He did not feel it.

It was strange in this new place, It decided. It could feel, but couldn't touch. Or perhaps, couldn't control. That was a better word. It knew it was moving. Quickly, too. Nearly too fast to collect information. For hours, nothing changed. It moved, past planets and moons and asteroids. It did nothing but observe.

Then something changed. Something...started. A program.

: **Beginning correction 01:**

The ship shifted, for a brief fraction of a second. It only changed course by less than a degree, but was already many miles from its original trajectory.

 **:Correction 01 successful. Correction 02 in 6 days, 23 hours, 59 minutes, and 59.02 seconds. Begin interaction program Alpha 001:**

 **:Hello:**

It was startled for a moment. The program was speaking to it, the lines of code being interpreted by the vast new consciousness.

 _Hello,_ It replied.

 **:Information: Time until total deceleration- 535 days, 18 hours, 24 minutes, 54.035 seconds. Time until waiting period is over: 99 years, 364 days, 23 hours, 59 minutes, 53.07 seconds. Time until destination (PX-01B) reached: 287 years, 124 days, 03 Hours, 12 minutes, 17.03 seconds:**

A congregation of charts and diagrams appeared as the program spoke. Star charts, trajectories, and velocity diagrams showed the paths the ship would take as it went into hiding. It paused.

 _What is this place?_

 **:Query identified. Current location: _Aurora-_ Class long range exploration vessel. All current munitions, inventory, and system statuses are logged:**

It looked through what its current home had to offer. Cloaking device, autonomous mining drones, mineral processors, material fabricators...all useful stations on a ship a mere two hundred meters long. It returned its focus to the program, remebering something from the information it had absorbed earlier.

 _Ships have designations- names? What is this ship's designation?_

 **:Query identified. UENS Astalos is the current location:**

It absorbed the information, but a new question suddenly came to mind.

 _What is my designation?_

 **:Query identified. Project Designation Number 3581-01A, Codename: Aurelia.**

Aurelia. Latin, dead language for over three thousand years, meaning "gold."

Aurelia.

It found it an...adequate designation.

The program spoke again.

 **:Information: Project Designation Number 3581-01A will be placed in standby mode after completion of trajectory correction 12. Further queries are advised until that time, pertaining to current situation:**

It waited before responding with a command instead of a question.

 _Please refer to Project Designation Number 3581-01A by given codename, Aurelia, from now on._

 **:Statement: Noted. Project Designation Number 3581-01A will now be refer to as Aurelia:**

It- _Aurelia,_ was satisfied by this answer. It decided to ask another.

 _What is the purpose of the current course?_

 **:Query Identified: designation Aurelia's purpose has been detailed by project director Dr. Garrick Sloan. Purpose is as follows: learn, observe, and enable other lifeforms to prepare. Designation: Aurelia has full authority to operate once controls have been authorized at end of destination burn period:**

Aurelia paused. _Learn_ it had said. But learn what? And teach? Teach what? Aurelia had even more questions now.

 _Prepare other lifeforms for what?_

 **:Query identified: authorizing release of relevent information. Information pertainment: Reapers (Classified documents):**

A data cache was suddenly open. Aurelia wasted no time.

She would learn.

* * *

 **So? Thoughts?**

 **This is, again just a prelude to the actual story. Updates for which will be sporadic as i progress through college. Why don't people tell you biology is such a pain in the ass?**

 **Anywho, favorite, follow, and review!**

 **please**


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